Euphausiids are a vital component of global marine micronekton. To reveal the primary environmental factors influencing euphausiid distribution patterns in the previously overlooked low-latitude ecosystems, we investigated a large-scale community structure of euphausiids covering the North Pacific subtropical gyre (NPSG) and low-latitude eastern Indian (EI), and South Pacific Oceans (SP). A total of 41 euphausiid species from six genera were identified. Integrated primary production (PP) correlated significantly with the euphausiid abundance and species diversity and displayed the most critical influence on the variations in euphausiid community structure in low latitudes. Dissolved oxygen (DO) was the second significant environmental driver. Due to the distinct distribution patterns of euphausiid species in response to different PP and DO levels, the low-latitude euphausiid assemblages were mainly distinguished into subtropical and tropical communities. The subtropical euphausiid community associated with lower PP and higher DO demonstrated significantly lower euphausiid abundance but higher diversity than the tropical community. Euphausia brevis, E. mutica, and Stylocheiron abbreviatum, which characterize the subtropical community, appear to depend less on the phytoplanktonic prey. Euphausia diomedeae and Hansarsia gracilis, typifying the tropical population, showed stronger hypoxia tolerance. Additionally, each community was further divided into three subgroups under the influence of surface PP (subtropical: marginal NPSG, central NPSG, and austral EI-SP subgroups; tropical: the Bay of Bengal, equatorial EI, and equatorial EI-SP subgroups). These results suggested that food resource is the most important in shaping euphausiids’ community structure in an oligotrophic ecosystem with subtle hydrography gradients.